Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 62,963 bioRxiv papers from 279,321 authors.
Creating a universal SNP and small indel variant caller with deep neural networks
Pegah T. Afshar,
Sam S. Gross,
Cory Y. McLean,
Mark A. DePristo
Posted 14 Dec 2016
bioRxiv DOI: 10.1101/092890 (published DOI: 10.1038/nbt.4235)
Posted 14 Dec 2016
Next-generation sequencing (NGS) is a rapidly evolving set of technologies that can be used to determine the sequence of an individual's genome by calling genetic variants present in an individual using billions of short, errorful sequence reads. Despite more than a decade of effort and thousands of dedicated researchers, the hand-crafted and parameterized statistical models used for variant calling still produce thousands of errors and missed variants in each genome. Here we show that a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships (likelihoods) between images of read pileups around putative variant sites and ground-truth genotype calls. This approach, called DeepVariant, outperforms existing tools, even winning the "highest performance" award for SNPs in a FDA-administered variant calling challenge. The learned model generalizes across genome builds and even to other species, allowing non-human sequencing projects to benefit from the wealth of human ground truth data. We further show that, unlike existing tools which perform well on only a specific technology, DeepVariant can learn to call variants in a variety of sequencing technologies and experimental designs, from deep whole genomes from 10X Genomics to Ion Ampliseq exomes. DeepVariant represents a significant step from expert-driven statistical modeling towards more automatic deep learning approaches for developing software to interpret biological instrumentation data.
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